5/19/2022

Mox/Hyak is up and running!

Setup for categorical covariates (i.e., natal origin)

For our simulation, with three natal origins (JDR, YAK, and TUC)

Parameters:

  1. Grand mean = \(\beta_0\)
  2. Origin effect, JDR relative to TUC = \(\beta_{origin,1}\)
  3. Origin effect, YAK relative to TUC = \(\beta_{origin,2}\)

Effect of origin:

\[ JDR: \beta_0 + \beta_{origin,1} \\ YAK: \beta_0 + \beta_{origin,2} \\ TUC: \beta_0 - \beta_{origin,1} - \beta_{origin,2} \]

Interpretation is a bit funky

For example, in order for JDR origin fish to have a different movement probability than YAK and TUC origin fish, the following relationship must be followed:

\[ YAK = TUC \\ \beta_0 + \beta_{origin,2} = \beta_0 - \beta_{origin,1} - \beta_{origin,2} \\ 2 * \beta_{origin,2} = - \beta_{origin,1} \]

For example, \(\beta_0\) = 1, \(\beta_{origin,1}\) = -0.5 and \(\beta_{origin,2}\) = 0.25 would lead to these observed effects:

\[ JDR = 0.5 \\ YAK = 1.25 \\ TUC = 1.25 \]

Simulation model results

Origin only: b0

Origin only: borigin1

Origin only: borigin2

Run 4 - simulated dataset

##    origin rear               state2  n indices
## 1       1    1                 loss  5  [8,10]
## 2       1    2                 loss  5  [8,10]
## 3       2    1                 loss  3  [8,10]
## 4       2    2                 loss  1  [8,10]
## 5       3    1                 loss 34  [8,10]
## 6       3    2                 loss 43  [8,10]
## 7       1    1 mainstem, ICH to LGR 15   [8,5]
## 8       1    2 mainstem, ICH to LGR 20   [8,5]
## 9       3    1 mainstem, ICH to LGR 45   [8,5]
## 10      3    2 mainstem, ICH to LGR 74   [8,5]
##    origin rear               state2  n indices
## 1       1    1                 loss  3  [8,10]
## 2       1    2                 loss  3  [8,10]
## 3       2    1                 loss  2  [8,10]
## 4       2    2                 loss  2  [8,10]
## 5       3    1                 loss 24  [8,10]
## 6       3    2                 loss 40  [8,10]
## 7       1    1 mainstem, ICH to LGR 16   [8,5]
## 8       1    2 mainstem, ICH to LGR 24   [8,5]
## 9       2    1 mainstem, ICH to LGR  3   [8,5]
## 10      2    2 mainstem, ICH to LGR  4   [8,5]
## 11      3    1 mainstem, ICH to LGR 46   [8,5]
## 12      3    2 mainstem, ICH to LGR 41   [8,5]

Origin + rear: beta_0

Origin + rear: rear

Origin + rear: beta_origin1

Origin + rear: beta_origin2

Temperature only: beta_0

Temperature only: beta_temp

Temperature + flow - correlation issues?

Temperature + flow: b0

Temperature + flow: btemp

Temperature + flow: bflow

Temperature, flow, origin, and rear

Spill covariate

  • Binary variable (was there any spill around a window of time of the estimated transition date), or count of days of spill within window?